This paper discusses design and control of massively parallel microcantilever arrays with multiwalled carbon nanotube tips. It can be used for imaging, testing and 3D nanomanipulation of nanoparticles and biological samples. The microcantilever has a multiwalled carbon nanotube tip and four additional carbon nanotubes for 3D fine manipulation by electrostatic forces. The microcantilever is attached to a piezoelectric actuator that can be individually actuated. The reflected light from the deflected microcantilever is collected by a position sensitive photodetector and fast readout is achieved by a time-multiplexing scheme. A controller is proposed for nanomanipulation of samples and tapping mode operation based on a distributed parameter system model. The controller performance is shown via simulation.